-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_2502908-2700012

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.5585_t
Couldn't classify 65430, 65448
Couldn't classify 66489, 66515
Sorry, prediction pasa_asmbl_24273.p1 fails validation.
(GGG)	 CA	65430-65448	GT	TGG
(ACC)	 AG	65621-65785	GT	AGG
(CCC)	 AG	66132-66307	GT	AGG
(GTG)	 AG	66489-66515	GA	ACG
-recovered pasa_asmbl_24273.p1, internal, 65621, 65785
-recovered pasa_asmbl_24273.p1, internal, 66132, 66307
Valid prediction for GeneMark_model.5619_t
Valid prediction for Augustus_model.g2306.t1
Couldn't classify 70282, 70307
Couldn't classify 72420, 72536
Sorry, prediction pasa_asmbl_24275.p1 fails validation.
(GCC)	 AG	70282-70307	GT	AGG
(GTA)	 AG	70732-70852	GT	AGG
(GCG)	 AG	71174-71255	GT	CGG
(ACT)	 AG	71571-71735	GT	TGG
(GAG)	 AG	71913-72037	GT	AGG
(GTG)	 AG	72420-72536	AG	GTA
-recovered pasa_asmbl_24275.p1, internal, 70282, 70307
-recovered pasa_asmbl_24275.p1, internal, 70732, 70852
-recovered pasa_asmbl_24275.p1, internal, 71174, 71255
-recovered pasa_asmbl_24275.p1, internal, 71571, 71735
-recovered pasa_asmbl_24275.p1, internal, 71913, 72037
Valid prediction for GeneMark_model.5576_t
Valid prediction for GlimmerHMM_glimmerT_3460-T1
Valid prediction for GeneMark_model.5574_t
Valid prediction for Augustus_model.g2301.t1
Valid prediction for GeneMark_model.5620_t
Valid prediction for snap_scaffold_2-snap.602-T1
Valid prediction for GeneMark_model.5617_t
Valid prediction for GlimmerHMM_glimmerT_3455-T1
Valid prediction for Augustus_model.g2304.t1
Valid prediction for snap_scaffold_2-snap.592-T1
Valid prediction for GeneMark_model.5590_t
Valid prediction for snap_scaffold_2-snap.617-T1
Valid prediction for GeneMark_model.5606_t
Valid prediction for GeneMark_model.5598_t
Valid prediction for GlimmerHMM_glimmerT_3471-T1
Couldn't classify 77106, 77175
Couldn't classify 79920, 80110
Sorry, prediction pasa_asmbl_25484.p1 fails validation.
(CTG)	 AC	77106-77175	GT	AGG
(CAG)	 AG	77435-77583	GT	GGG
(ATG)	 AG	77928-78119	GT	TGG
(GCC)	 AG	78511-78632	GT	AGG
(GAT)	 AG	78905-79043	GT	AGG
(GTG)	 AG	79277-79397	GT	TGG
(GGG)	 AG	79920-80110	GC	TTG
-recovered pasa_asmbl_25484.p1, initial, 77928, 78119
-recovered pasa_asmbl_25484.p1, internal, 77435, 77583
-recovered pasa_asmbl_25484.p1, internal, 77928, 78119
-recovered pasa_asmbl_25484.p1, internal, 78511, 78632
-recovered pasa_asmbl_25484.p1, internal, 78905, 79043
-recovered pasa_asmbl_25484.p1, internal, 79277, 79397
-recovered pasa_asmbl_25484.p1, internal, 79920, 80110
Valid prediction for snap_scaffold_2-snap.607-T1
Valid prediction for GeneMark_model.5630_t
Valid prediction for snap_scaffold_2-snap.613-T1
Valid prediction for GeneMark_model.5588_t
Couldn't classify 99911, 100252
Sorry, prediction pasa_asmbl_22935.p1 fails validation.
(TCT)	 TC	99911-100252	AT	AAA
Valid prediction for GeneMark_model.5578_t
Valid prediction for GlimmerHMM_glimmerT_3468-T1
Valid prediction for snap_scaffold_2-snap.600-T1
Valid prediction for snap_scaffold_2-snap.609-T1
Valid prediction for snap_scaffold_2-snap.603-T1
Valid prediction for GlimmerHMM_glimmerT_3462-T1
Valid prediction for snap_scaffold_2-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_3472-T1
Valid prediction for snap_scaffold_2-snap.610-T1
Valid prediction for GeneMark_model.5613_t
Valid prediction for snap_scaffold_2-snap.611-T1
Valid prediction for GeneMark_model.5610_t
Couldn't classify 22382, 22409
Couldn't classify 24135, 24257
Sorry, prediction pasa_asmbl_24268.p1 fails validation.
(GAA)	 CG	22382-22409	GT	AGG
(ATG)	 AG	22492-22596	GT	CTG
(CCT)	 AG	22836-22992	GT	CGG
(CCC)	 AG	23543-23615	GT	AGG
(GTG)	 AG	24135-24257	GG	GGG
add_exon() Sorry, pasa_asmbl_24268.p1 22492-22596-initial-1 is invalid.
-recovered pasa_asmbl_24268.p1, initial, 22492, 22596
-recovered pasa_asmbl_24268.p1, internal, 22492, 22596
-recovered pasa_asmbl_24268.p1, internal, 22836, 22992
-recovered pasa_asmbl_24268.p1, internal, 23543, 23615
Valid prediction for Augustus_model.g2298.t1
Valid prediction for GlimmerHMM_glimmerT_3452-T1
Valid prediction for GeneMark_model.5633_t
Valid prediction for GeneMark_model.5596_t
Valid prediction for GeneMark_model.5600_t
Couldn't classify 75787, 75975
Couldn't classify 76383, 76508
Sorry, prediction pasa_asmbl_25406.p2 fails validation.
(GTG)	 AA	75787-75975	GT	AGG
(GTC)	 AG	76383-76508	TC	GGT
Valid prediction for GeneMark_model.5581_t
Valid prediction for snap_scaffold_2-snap.616-T1
Valid prediction for GeneMark_model.5635_t
Valid prediction for GlimmerHMM_glimmerT_3465-T1
Valid prediction for GeneMark_model.5594_t
Valid prediction for GlimmerHMM_glimmerT_3459-T1
Valid prediction for GeneMark_model.5615_t
Valid prediction for GeneMark_model.5604_t
Valid prediction for GlimmerHMM_glimmerT_3464-T1
Valid prediction for snap_scaffold_2-snap.612-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.5602_t
Valid prediction for snap_scaffold_2-snap.584-T1
Valid prediction for Augustus_model.g2300.t1
Valid prediction for snap_scaffold_2-snap.619-T1
Valid prediction for GeneMark_model.5580_t
Valid prediction for GeneMark_model.5608_t
Valid prediction for GlimmerHMM_glimmerT_3450-T1
Valid prediction for GlimmerHMM_glimmerT_3456-T1
Valid prediction for GeneMark_model.5622_t
Valid prediction for snap_scaffold_2-snap.596-T1
Valid prediction for GeneMark_model.5611_t
Valid prediction for GeneMark_model.5626_t
Valid prediction for GlimmerHMM_glimmerT_3466-T1
Valid prediction for GeneMark_model.5624_t
Valid prediction for snap_scaffold_2-snap.586-T1
Valid prediction for GeneMark_model.5628_t
Couldn't classify 80315, 80444
Sorry, prediction pasa_asmbl_25422.p1 fails validation.
(CAG)	 AG	80315-80444	GT	AGG
(ACC)	 AG	80526-80689	GT	AGG
(CTG)	 AG	81144-81273	GT	CTG
(ACG)	 AG	81678-81806	GT	TGG
(ACT)	 AG	81966-82042	GT	AGG
(CTG)	 AG	82442-82594	GA	GAG
-recovered pasa_asmbl_25422.p1, terminal, 82442, 82594
-recovered pasa_asmbl_25422.p1, internal, 80315, 80444
-recovered pasa_asmbl_25422.p1, internal, 80526, 80689
-recovered pasa_asmbl_25422.p1, internal, 81144, 81273
-recovered pasa_asmbl_25422.p1, internal, 81678, 81806
-recovered pasa_asmbl_25422.p1, internal, 81966, 82042

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GlimmerHMM_glimmerT_3470-T1
Valid prediction for GeneMark_model.5616_t
Valid prediction for GeneMark_model.5634_t
Valid prediction for snap_scaffold_2-snap.598-T1
Valid prediction for GeneMark_model.5603_t
Valid prediction for GeneMark_model.5618_t
Valid prediction for GlimmerHMM_glimmerT_3469-T1
Valid prediction for GeneMark_model.5605_t
Valid prediction for pasa_asmbl_22934.p1
Valid prediction for snap_scaffold_2-snap.601-T1
Valid prediction for GeneMark_model.5629_t
Valid prediction for GeneMark_model.5623_t
Valid prediction for snap_scaffold_2-snap.608-T1
Valid prediction for HiQ_model.g2307.t1
Valid prediction for GeneMark_model.5575_t
Valid prediction for GeneMark_model.5595_t
Valid prediction for GlimmerHMM_glimmerT_3457-T1
Valid prediction for snap_scaffold_2-snap.583-T1
Valid prediction for snap_scaffold_2-snap.618-T1
Valid prediction for GlimmerHMM_glimmerT_3458-T1
Valid prediction for GlimmerHMM_glimmerT_3453-T1
Valid prediction for snap_scaffold_2-snap.591-T1
Valid prediction for GeneMark_model.5579_t
Valid prediction for snap_scaffold_2-snap.614-T1
Valid prediction for snap_scaffold_2-snap.588-T1
Valid prediction for Augustus_model.g2310.t1
Valid prediction for GeneMark_model.5627_t
Valid prediction for GeneMark_model.5625_t
Valid prediction for snap_scaffold_2-snap.593-T1
Valid prediction for GeneMark_model.5597_t
Valid prediction for GeneMark_model.5587_t
Valid prediction for GeneMark_model.5607_t
Valid prediction for snap_scaffold_2-snap.595-T1
Valid prediction for Augustus_model.g2299.t1
Valid prediction for HiQ_model.g2305.t1
Valid prediction for snap_scaffold_2-snap.599-T1
Valid prediction for Augustus_model.g2311.t1
Valid prediction for Augustus_model.g2312.t1
Valid prediction for snap_scaffold_2-snap.585-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.5582_t
Valid prediction for snap_scaffold_2-snap.594-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.5632_t
Valid prediction for GeneMark_model.5601_t
Valid prediction for GeneMark_model.5584_t
Valid prediction for GlimmerHMM_glimmerT_3474-T1
Valid prediction for GlimmerHMM_glimmerT_3463-T1
Valid prediction for GeneMark_model.5614_t
Valid prediction for snap_scaffold_2-snap.590-T1
Valid prediction for CodingQuarry_transcript_28413-T1
Valid prediction for CodingQuarry_transcript_28418-T1
Valid prediction for GeneMark_model.5589_t
Valid prediction for GeneMark_model.5593_t
Valid prediction for GeneMark_model.5592_t
Valid prediction for GlimmerHMM_glimmerT_3461-T1
Valid prediction for snap_scaffold_2-snap.587-T1
Valid prediction for snap_scaffold_2-snap.615-T1
Valid prediction for GeneMark_model.5612_t
Valid prediction for Augustus_model.g2303.t1
Valid prediction for GeneMark_model.5577_t
Valid prediction for CodingQuarry_transcript_28412-T1
Valid prediction for GlimmerHMM_glimmerT_3473-T1
Valid prediction for GeneMark_model.5637_t
Valid prediction for snap_scaffold_2-snap.604-T1
Valid prediction for GeneMark_model.5583_t
Valid prediction for GeneMark_model.5609_t
Valid prediction for snap_scaffold_2-snap.589-T1
Valid prediction for GeneMark_model.5636_t
Valid prediction for HiQ_model.g2302.t1
Valid prediction for Augustus_model.g2309.t1
Valid prediction for Augustus_model.g2308.t1
Valid prediction for GeneMark_model.5599_t
Valid prediction for GeneMark_model.5586_t
Valid prediction for pasa_asmbl_22924.p1
Valid prediction for pasa_asmbl_22932.p1
Valid prediction for GeneMark_model.5621_t
Valid prediction for GlimmerHMM_glimmerT_3451-T1
Valid prediction for snap_scaffold_2-snap.605-T1
Valid prediction for GlimmerHMM_glimmerT_3467-T1
Valid prediction for CodingQuarry_transcript_28417-T1
Valid prediction for pasa_asmbl_22925.p1
Valid prediction for CodingQuarry_transcript_28415-T1
Valid prediction for GlimmerHMM_glimmerT_3454-T1
Valid prediction for CodingQuarry_transcript_28416-T1
Valid prediction for snap_scaffold_2-snap.597-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9945, rend_intergenic: 4916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36422, rend_intergenic: 18653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58636, rend_intergenic: 50696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65531, rend_intergenic: 63230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82594, rend_intergenic: 65665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88618, rend_intergenic: 85067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128211, rend_intergenic: 91587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134058, rend_intergenic: 128337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140105, rend_intergenic: 135081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152034, rend_intergenic: 149268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166764, rend_intergenic: 153338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173918, rend_intergenic: 171256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181252, rend_intergenic: 174041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188302, rend_intergenic: 181728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197105
-exon list size: 888


building trellis

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59.2    
59.3    
59.4    
59.6    
59.7    
59.8    
59.9    
60.0    
60.1    
60.2    
60.3    
60.4    
60.6    
60.7    
60.8    
60.9    
61.0    
61.1    
61.2    
61.3    
61.5    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.4    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.1    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.2    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
66.0    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.6    
99.7    
99.8    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9945, rend_intergenic: 4916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36422, rend_intergenic: 18653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58636, rend_intergenic: 50696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65531, rend_intergenic: 63230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82594, rend_intergenic: 65665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88618, rend_intergenic: 85067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128211, rend_intergenic: 91587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134058, rend_intergenic: 128337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140105, rend_intergenic: 135081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152034, rend_intergenic: 149268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166764, rend_intergenic: 153338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173918, rend_intergenic: 171256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181252, rend_intergenic: 174041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188302, rend_intergenic: 181728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support